Test Frequency Domain

display properties

BODY

set the 'nirfasterroot' as current folder

test FD on standard mesh:

forward data 2D

continuous wave 2D

data_cw = femdata_FD(mesh,0);

% plot intensity integrated @ all sources

plotimage(mesh,log10(abs(sum(data_cw.phi,2))));

title('CW: Total log10 Intensity /mm$^{-2}$s$^{-1}$','Interpreter','latex')

set(gca,'CLim',[-3 0])

% plot intensity for source-detector pairs

figure('Name',mesh.name)

semilogy(data_cw.amplitude,'o--')

title('Log10 Intensity','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('photon fluence rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

%calcuate source-detector distances

sd_distances = sqrt(sum((mesh.meas.coord(mesh.link(:,2),:) - mesh.source.coord(mesh.link(:,1),:)).^2,2));

% plot intensity vs source-detector distances

figure('Name',mesh.name)

semilogy(sd_distances, data_cw.amplitude,'.')

title('Log10 Intensity','Interpreter','latex');

xlabel('source-detector distance /mm','Interpreter','latex')

ylabel('photon fluence rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

frequency domain 2D

data_FD = femdata_FD(mesh,100e6);

% plot intensity integrated @ all sources

plotimage(mesh,log10(abs(sum(data_FD.phi,2))));

title('FD: Total log10 Intensity at 100MHz /mm$^{-2}$s$^{-1}$','Interpreter','latex');

set(gca,'CLim',[-3 0])

figure('Name',mesh.name)

% plot log intensity at source-detector pairs

subplot(2,1,1); semilogy(data_FD.amplitude,'o-')

title('Log10 Intensity at 100MHz','Interpreter','latex');

ylabel('phot. fl. rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

% plot phase shift at source-detector pairs

subplot(2,1,2); plot(data_FD.phase,'o-')

title('Phase at 100MHz','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('phase shift /deg','Interpreter','latex')

figure('Name',mesh.name)

% plot log intensity vs source-detector distance

subplot(2,1,1); semilogy(sd_distances, data_FD.amplitude,'.')

title('Log10 Intensity at 100MHz','Interpreter','latex');

ylabel('phot. fl. rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

% plot phase vs source-detector distance

subplot(2,1,2); plot(sd_distances, data_FD.phase,'.')

title('Phase at 100MHz','Interpreter','latex');

xlabel('source-detector distance /mm','Interpreter','latex')

ylabel('phase shift /deg','Interpreter','latex')

Jacobian 2D

%continuous wave

[J_cw,~] = jacobian_FD(mesh,0);

plotimage(mesh,J_cw.complete(12,:));

title('Single Jacobian: $\ln(I)/\mu_{\mathrm{a}}$ at CW','Interpreter','latex');

plotimage(mesh,sum(J_cw.complete,1));

title('Total Jacobian: $\ln(I)/\mu_{\mathrm{a}}$ at CW','Interpreter','latex');

%frequency domain

[J_FD,~] = jacobian_FD(mesh,100e6);

plotimage(mesh,J_FD.complete(11,1:end/2));

title('Single Jacobian: $\ln(I)/\kappa$ at FD','Interpreter','latex');

plotimage(mesh,J_FD.complete(11,end/2+1:end));

title('Single Jacobian: $\ln(I)/\mu_{\mathrm{a}}$ at FD','Interpreter','latex');

plotimage(mesh,J_FD.complete(12,1:end/2));

title('Single Jacobian: Phase/$\kappa$ at FD','Interpreter','latex');

plotimage(mesh,J_FD.complete(12,end/2+1:end));

title('Single Jacobian: Phase/$\mu_{\mathrm{a}}$ at FD','Interpreter','latex');

forward data 3D

continuous wave 3D

data_cw = femdata_FD(mesh,0);

plotimage(mesh,log10(abs(sum(data_cw.phi,2))));

title('CW: Total log10 Intensity /mm$^{-2}$s$^{-1}$','Interpreter','latex')

set(gca,'CLim',[-8 0])

figure('Name',mesh.name)

%plot intensities at source-detector pairs

semilogy(data_cw.amplitude,'o--')

title('Log10 Intensity','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('photon fluence rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

%calcuate source-detector distances

sd_distances = sqrt(sum((mesh.meas.coord(mesh.link(:,2),:) - mesh.source.coord(mesh.link(:,1),:)).^2,2));

% plot intensity vs source-detector distances

figure('Name',mesh.name)

semilogy(sd_distances, data_cw.amplitude,'.')

title('Log10 Intensity','Interpreter','latex');

xlabel('source-detector distance /mm','Interpreter','latex')

ylabel('photon fluence rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

frequency domain 3D

data_FD = femdata_FD(mesh,100e6);

% plot intensity integrated @ all sources

plotimage(mesh,log10(abs(sum(data_FD.phi,2))));

title('FD: Total log10 Intensity at 100MHz /mm$^{-2}$s$^{-1}$','Interpreter','latex');

set(gca,'CLim',[-8 0])

figure('Name',mesh.name)

% plot log intensity at source-detector pairs

subplot(2,1,1); semilogy(data_FD.amplitude,'o-')

title('Log10 Intensity at 100MHz','Interpreter','latex');

ylabel('phot. fl. rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

% plot phase shift at source-detector pairs

subplot(2,1,2); plot(data_FD.phase,'o-')

title('Phase at 100MHz','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('phase shift /deg','Interpreter','latex')

figure('Name',mesh.name)

% plot log intensity vs source-detector distance

subplot(2,1,1); semilogy(sd_distances, data_FD.amplitude,'.')

title('Log10 Intensity at 100MHz','Interpreter','latex');

ylabel('phot. fl. rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

% plot phase vs source-detector distance

subplot(2,1,2); plot(sd_distances, data_FD.phase,'.')

title('Phase at 100MHz','Interpreter','latex');

xlabel('source-detector distance /mm','Interpreter','latex')

ylabel('phase shift /deg','Interpreter','latex')

Jacobian 3D

%continuous wave

[J_cw,~] = jacobian_FD(mesh,0);

plotimage(mesh,J_cw.complete(12,:));

title('Single Jacobian: $\ln(I)/\mu_{\mathrm{a}}$ at CW','Interpreter','latex');

alpha(0.1)

plotimage(mesh,sum(J_cw.complete,1));

title('Total Jacobian: $\ln(I)/\mu_{\mathrm{a}}$ at CW','Interpreter','latex');

alpha(0.1)

%frequency domain

[J_FD,~] = jacobian_FD(mesh,100e6);

plotimage(mesh,J_FD.complete(11,1:end/2));

title('Single Jacobian: $\ln(I)/\kappa$ at FD','Interpreter','latex');

alpha(0.1)

plotimage(mesh,J_FD.complete(11,end/2+1:end));

title('Single Jacobian: $\ln(I)/\mu_{\mathrm{a}}$ at FD','Interpreter','latex');

alpha(0.1)

plotimage(mesh,J_FD.complete(12,1:end/2));

title('Single Jacobian: Phase/$\kappa$ at FD','Interpreter','latex');

alpha(0.1)

plotimage(mesh,J_FD.complete(12,end/2+1:end));

title('Single Jacobian: Phase/$\mu_{\mathrm{a}}$ at FD','Interpreter','latex');

alpha(0.1)

test FD on spectral mesh:

forward data 2D, spectral

continuous wave 2D, spectral

data_cw = femdata_FD(mesh,0);

plotimage(mesh,log10(abs(sum(data_cw.phi(:,:,2),2))));

title('CW: Total log10 Intensity at 2nd wavelength /mm$^{-2}$s$^{-1}$','Interpreter','latex');

set(gca,'CLim',[-3 0])

figure('Name',mesh.name)

%plot intensities at source-detector pairs

semilogy(data_cw.amplitude,'.-')

title('Log10 Intensity - spectral','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('photon fluence rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

legend(num2str(mesh.wv),'Interpreter','latex')

frequency domain 2D, spectral

data_FD = femdata_FD(mesh,100e6);

plotimage(mesh,log10(abs(sum(data_FD.phi(:,:,2),2))));

title('FD: Total log10 Intensity at 100MHz at 2nd wavelength /mm$^{-2}$s$^{-1}$','Interpreter','latex');

set(gca,'CLim',[-3 0])

figure('Name',mesh.name)

% plot log intensity at source-detector pairs

subplot(2,1,1); semilogy(data_FD.amplitude,'.-')

title('Log10 Intensity at 100MHz - spectral','Interpreter','latex');

ylabel('phot. fl. rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

legend(num2str(mesh.wv),'Interpreter','latex')

% plot phase shift at source-detector pairs

subplot(2,1,2); plot(data_FD.phase,'.-')

title('Phase at 100MHz - spectral','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('phase shift /deg','Interpreter','latex')

legend(num2str(mesh.wv),'Interpreter','latex')

Jacobian 2D, spectral

%continuous wave

[J_cw,~] = jacobian_FD(mesh,0);

plotimage(mesh,J_cw(12,1:end/3));

title('Single Jacobian: $\ln(I)/C_{1}$ at CW','Interpreter','latex');

plotimage(mesh,sum(J_cw(:,end/3+1:2*(end/3)),1));

title('Total Jacobian: $\ln(I)/C_{2}$ at CW','Interpreter','latex');

%frequency domain

[J_FD,~] = jacobian_FD(mesh,100e6);

plotimage(mesh,J_FD(11,1:end/5));

title('Single Jacobian: $\ln(I)/C_{1}$ at FD','Interpreter','latex');

plotimage(mesh,J_FD(11,end/5+1:2*(end/5)));

title('Single Jacobian: $\ln(I)/C_{2}$ at FD','Interpreter','latex');

plotimage(mesh,J_FD(12,2*(end/5)+1:3*(end/5)));

title('Single Jacobian: Phase/$C_{3}$ at FD','Interpreter','latex');

plotimage(mesh,J_FD(12,3*end/5+1:4*(end/5)));

title('Single Jacobian: Phase/$S_{\mathrm{a}}$ at FD','Interpreter','latex');

forward data 3D, spectral

continuous wave 3D, spectral

data_cw = femdata_FD(mesh,0);

plotimage(mesh,log10(abs(sum(data_cw.phi(:,:,7),2))));

title('CW: Total log10 Intensity at last wavelength /mm$^{-2}$s$^{-1}$','Interpreter','latex')

set(gca,'CLim',[-8 0])

figure('Name',mesh.name)

%plot intensities at source-detector pairs

semilogy(data_cw.amplitude,'o--')

title('Log10 Intensity','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('photon fluence rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

frequency domain 3D, spectral

data_FD = femdata_FD(mesh,100e6);

plotimage(mesh,log10(abs(sum(data_FD.phi(:,:,7),2))));

title('FD: Total log10 Intensity at 100MHz at last wavelength /mm$^{-2}$s$^{-1}$','Interpreter','latex');

set(gca,'CLim',[-8 0])

figure('Name',mesh.name)

% plot log intensity at source-detector pairs

subplot(2,1,1); semilogy(data_FD.amplitude,'.-')

title('Log10 Intensity at 100MHz - spectral','Interpreter','latex');

ylabel('phot. fl. rate /mm$^{-2}$s$^{-1}$','Interpreter','latex')

legend(num2str(mesh.wv),'Interpreter','latex')

% plot phase shift at source-detector pairs

subplot(2,1,2); plot(data_FD.phase,'.-')

title('Phase at 100MHz - spectral','Interpreter','latex');

xlabel('source-detector pair /-','Interpreter','latex')

ylabel('phase shift /deg','Interpreter','latex')

legend(num2str(mesh.wv),'Interpreter','latex')

Jacobian 3D, spectral

%continuous wave

[J_cw,~] = jacobian_FD(mesh,0);

plotimage(mesh,J_cw(12,1:end/3));

title('Single Jacobian: $\ln(I)/C_{1}$ at CW','Interpreter','latex');

alpha(0.1)

plotimage(mesh,sum(J_cw(:,end/3+1:2*(end/3)),1));

title('Total Jacobian: $\ln(I)/C_{2}$ at CW','Interpreter','latex');

alpha(0.1)

%frequency domain

[J_FD,~] = jacobian_FD(mesh,100e6);

plotimage(mesh,J_FD(11,1:end/5));

title('Single Jacobian: $\ln(I)/C_{1}$ at FD','Interpreter','latex');

alpha(0.1)

plotimage(mesh,J_FD(11,end/5+1:2*(end/5)));

title('Single Jacobian: $\ln(I)/C_{2}$ at FD','Interpreter','latex');

alpha(0.1)

plotimage(mesh,J_FD(12,2*(end/5)+1:3*(end/5)));

title('Single Jacobian: Phase/$C_{3}$ at FD','Interpreter','latex');

alpha(0.1)

plotimage(mesh,J_FD(12,3*end/5+1:4*(end/5)));

title('Single Jacobian: Phase/$S_{\mathrm{a}}$ at FD','Interpreter','latex');

alpha(0.1)